We are told that, shortly after midnight on 24 June, 2016, when the European Union referendum result was declared, David Cameron and George Osborne – the true begetters of the squalid exercise in party management – were as surprised as they were disappointed. That was because they did not understand the character of the English people. They took it for granted that votes would be cast according to a calculation of whether membership of the European Union or withdrawal offered England the most prosperous future. But inhabitants of this fortress built by nature do not live by GDP alone.

Many of them have an ingrained belief in national sovereignty. England is at its best, the argument runs, when it is neither governed nor influenced by decisions taken in what Shakespeare called “less happier lands”. If Cameron and Osborne had understood the causes and progress of the English Reformation they would have realised the appeal of “very well then, alone”. The parallels are far from exact, but they are near enough to prove that the English believe in deciding things for themselves.

Although there was no accession treaty, the church in England took a formal decision to affiliate to the Church of Rome. At the Synod of Whitby in 664, the assembled clergy of Northumberland – a far larger area than the modern county – decided to adopt the Roman liturgy and the Roman calendar.

The rest of England followed suit and the unified Catholic Church was created. It remained happily subservient to Rome for nearly 900 years – rather longer than Britain maintained its allegiance to the Common Market that became the European Union.

Towards the end of the long affiliation, there were critics of the compact. John Wycliffe and William Tyndale objected to the imposition of restraints and regulations – in their case the prohibition of English language translations of the Bible. But most of England was satisfied that Rome was on their side as well as God’s. In 1144 an Englishman – Nicholas Breakspear who became Adrian IV – had been elected pope, a sure sign of respect. He had immediately demonstrated the value of association with supranational alliances by ceding the ownership of Ireland to Henry II.

Henry VIII was not so lucky. His hopes of becoming Holy Roman emperor were dashed when Cardinal Wolsey – who was expected to clear the way – was twice defeated in papal elections. Then the pope, ignoring England’s claim, divided South America between Spain and Portugal. Previously devout believers in the Roman connection began to realise, as disillusioned Common Marketers discovered, that membership of an international organisation requires give as well as take. But to abandon Rome – though not as big a risk as abandoning the EU – was a gamble with England’s future. Leavers claimed desirable alternatives were on offer. Martin Luther and Ulrich Zwingli advocated variants of the Protestant faith that, by their nature, accommodated what George Bernard Shaw, in Saint Joan, called “heresy nationalism”.

Pressure for a clean break with the pope was hardened by the alleged behaviour of the men in the Vatican who interfered in England’s affairs – just as EU officials in Brussels are accused of living in luxury at the expense of British taxpayers. Critics of the life in Rome included Reginald Pole – a future cardinal and chief minister to Mary Tudor – who the Daily Mail would have called “the Vatican whistleblower”. He left the Eternal City after a week. “Having seen the abomination of the cardinals, bishops and other offices, he could no wise tarry there any longer.” The reasons for dissatisfaction were mostly too complicated to be appreciated by what was then known as the common people. Annates and “first fruit” taxes were as difficult to understand in the 16th century as were monetary compensation amounts in the 20th. But the mystery about how Rome spent England’s money added to the resentment.

When the pope refused to endorse Henry’s divorce from Catherine of Aragon and make possible his marriage to Anne Boleyn, the king’s hubris allowed no other response than that he determined to be “both pope and emperor in his own kingdom”. But what is popularly regarded as the cause of the Reformation was no more than its occasion. And the great schism had very little to do with religion. The cause was essentially political.

Henry had willingly contributed to the campaign of vilification that followed Luther publicly burning the papal bull that excommunicated him, and the king remained a true believer in the basic doctrine of the Catholic Church. He remained reluctant to break with the religion, as distinct from the authority, of Rome. His dispute with the pope began in 1527, but full independence from Rome was not confirmed until the Acts of Supremacy and Succession became law in 1534. The early years of that interregnum were passed in what amounted to an unsuccessful attempt to renegotiate the relationship between London and Rome.

The king’s emissaries tried to demonstrate that Catholic teaching – the gospels and the writings of the early fathers – allowed Henry to remarry and remain in good standing within the church. It was only after his arguments were dismissed that he stopped burning men for questioning the pope’s teaching and started burning them for supporting the pope’s authority. And towards the end of his life he was so anxious to demonstrate his adherence to Catholic doctrine that he presided over the trial of John Lambert, convicted him of denying Christ’s real presence during the eucharist and watched while he was roasted to death, like a pig on a spit. Henry wanted a “soft” Reformation.

It was his daughter, Elizabeth, who made the Reformation “hard”. It is possible to argue that she had good personal cause. During the reign of Mary, her Catholic half-sister, there was a real possibility of her Protestant beliefs being mistaken for treason – punishable by death. And after her accession, the papal bull Regnans in Excelsis pronounced it lawful to assassinate the “pretend queen”.

Whatever the reason, Elizabeth determined, when possible, to eliminate Catholicism from her realm and, where elimination was not possible, to suppress it. Her punitive policies – the expulsion of priests, the denial of property rights, the desecration of churches and the prohibition of the Latin mass – were popularised by the belief that England was under threat from Catholic Europe and that had the several armadas not been defeated by English seamanship and weather, English Catholics would have welcomed and supported the invasion. The spirit of the age was articulated in the works of Shakespeare, which in turn influenced the English vision of England for the next 500 years. “Nought shall make us rue, if England to itself do rest but true.” It might have been the battle cry of the Brexiters. The idea it embodied certainly helped them to win the referendum campaign.

• The Catholics – The Church and Its People in Britain and Ireland from the Reformation to the Present Day is published by Chatto. To order a copy for £21.25 (RRP £25) go to bookshop.theguardian.com or call 0330 333 6846. Free UK p&p over £10, online orders only. Phone orders min p&p of £1.99.